Strategies for multiple sequence alignment |
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Authors: | Nicholas Hugh B Ropelewski Alexander J Deerfield David W |
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Affiliation: | Pittsburgh Supercomputing Center, Carnegie Mellon University, PA 15213, USA. nicholas@psc.edu |
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Abstract: | We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence alignment, followed by a discussion of the algorithms implemented within a variety of multiple sequence alignment programs. We also discuss additional alignment details such as gap penalty and distance metrics. The paper concludes with a discussion on how to improve alignment quality and the limitations of the techniques described in this paper |
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